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PDB40-Poster-Abstracts.Pdf Conference Program S T C A R T S B A PDB40 R Symposium E T October 28-30, 2011 S O Cold Spring Harbor Laboratory P Grace Auditorium POSTER PRESENTATIONS PDB40 posters will follow the numbers assigned in this abstract book. Poster locations will be numbered at the meeting site. Posters should be displayed throughout the meeting. A dedicated poster session is scheduled for Saturday, October 29, 2011 at 5:30 p.m., but meeting attendees are strongly encouraged to explore the posters throughout the meeting. Posters should fit within 1.22m x 1.22m (4 ft X 4 ft). Supplies for hanging posters will be provided. Poster Assignments * denotes travel award recipient Poster # Author Poster title 1* Hiromi Arai Crystal structure of a conformation-dependent rabbit IgG Fab fragment specific for a sequence-independent generic epitope associated with prefibrillar amyloid oligomers 2* Ryoichi Arai Domain-swapped dimeric structure of a de novo 4-helix bundle protein, WA20 3* Pelin Armutlu A TOG: -tubulin complex structure suggests conformation-based mechanisms for a microαtuβ bule polymerase 4 Christopher Bahl The Pseudomonas virulence factor Cif alters human ABC transporter trafficking and stability through epoxide hydrolase enzyme activity 5 Ramanuj Banerjee Threaded dimer assembly of the novel Psu fold from Enterobacteria phage P4 6* Avraham Ben-Shimon Deciphering the arginine-binding preferences of Ser/Thr kinases by computational surface mapping 7 Talapady Bhat Managing 2D and 3D ligand fragments from PDB and PubChem 8 Shveta Bisht Escherichia coli Diaminopropionate ammonia lyase—Structure, substrate specificity and catalysis 9* Spencer Bliven A comprehensive comparison of protein structures and the correlation of structure with function 10 Matthias Buck Dynamic protein-protein complexes—How alternative interactions create ensembles and how solution NMR and MD simulations can characterize them 11 Brianne Burkinshaw Salmonella virulence protein SopB down-regulates activity of host Rho GTPase Cdc42 by mimicking a nucleotide dissociation inhibitor 12* Arindam Chakrabarty Unique crystal structure of protozoan parasite Entamoeba histolytica malic enzyme 13* Tammy Cheng Structural biology meets systems biology—Gauging the systemic impact of single nucleotide polymorphisms 14* Alvaro Cortes AtlasCBS—A web server to graphically represent the content of chemico-biological databases I Poster # Author Poster title 15 Charles Dann III Treatment of cancer and autoinflammatory disease for over sixty years—Structural basis for folate and antifolate trafficking via human folate receptors 16* Teresa De la Mora Crystal structures of eIF4E in complex with Bn 7-GMP 17* Bryan Der Metal-mediated affinity and orientation specificity in a computationally designed protein homodimer 18 Jianping Ding Regulation of the histone acetyltransferase activity of hMOF via autoacetylation of Lys274 19 Wolfgang Dostmann A structural analysis of the regulatory domain from the cGMP-dependent protein kinase I α 20 Joseph Dybas Evolution of protein structures from the perspective of their super-secondary structure building blocks 21* Clarissa Eibl Crystal structure of NLRP4 pyrin domain 22 Richard Feldmann The second log 23 Javier Fernandez-Martinez Structure-function Map of a heptameric module in the nuclear pore complex 24 Barry Finzel The use of distance geometry for substructure searching and local superposition in DNA, RNA, and protein-polynucleotide complexes 25 Andras Fiser Predicting protein structure with supersecondary-structure building blocks and basic NMR data 26* Szu-Chin Fu Prediction of leucine-rich nuclear export signal containing proteins with NESsential 27* Kyoko Furuita NMR structural studies of the complex between lipid binding protein OSBP and ER membrane protein VAP-A 28 Miwako Homma Autophosphorylation of CK2 at the N-terminal region is required for its α catalytic activity 29* Corey Hryc Hybrid de novo modeling for 4 Å resolution cryo-EM maps of viruses 30 Valentin Ilyin PFAT—Protein Functional Annotation based on TOPOFIT 31 Valentin Ilyin N-TOPOFIT-DB, a DNA / RNA 3-D structural alignment database by N-TOPOFIT 32 Hitoshi Inada Structure of human TRPV4 ankyrin repeat domain 33 Constance Jeffery Moonlighting proteins 34* Fangling Ji Solution NMR and biophysical analysis of the cataract-associated R76S mutant of human D-crystallin γ 35 Holly Jing Discovery of novel inhibitors of therapeutic targets using fragment-based lead discovery methods 36 Jan Johansson Prevention of amyloid -peptide fibrillation—Insights from the BRICHOS domain β structure 37 Chisa Kamada Supercomputational life science in Japan 38 Tatsuki Kashiwagi Crystallization of proteins in high magnetic force fields aiming at high resolution structures 39 Takeshi Kawabata Chemical similarity-based docking to receptor proteins by searching maximum common substructure 40 Choel Kim Structural and biochemical studies of the cGMP selectivity for cGMP dependent protein kinase 41* Seung Joong Kim Integrative structure determination of the components of the nuclear pore complex by X-ray crystallography, small angle X-Ray scattering, electron microscopy, NMR and comparative modeling II Poster # Author Poster title 42* Serah Kimani Unexpected reactions resulting from mutating catalytic residues in an amidase reveal the role of the catalytic unit 43* Yu Kitago Structural basis for peptide ligand recognition by LR11 Vps10p domain 44 Stefan Knight Structural basis for control of spider silk assembly—A conserved N-terminal solubility relay 45 Adrian Laurenzi Improving EST annotation with protein structure prediction software 46 Tali Lavy The GAL regulon in S. cerevisiae —The Gal3p/Gal80p interaction 47 Thomas Leeper Silver (I) mellatated protein structures derived by combined NMR and X-ray crystallographic analyses 48 Yang Lei A maximum-likelihood approach to local real-space model fitting 49* Alejandra Leo-Macias In vitro reconstituted F-actin and fascin bundles studied by cryoelectron tomography and subtomogram averaging 50* Yunfeng Li Crystal structure and functional studies of the GerBC component of a Bacillus subtilis spore germination receptor 51* Vidya Mangala Prasad Towards a structure for the Rubella virus capsid protein 52 Manish Manish Computational design of conformationally intact immunogen for the elicitation of protective antibody immune response 53 Stefano Maria Marino Extreme evolutionary pressure determines Cysteine residues distribution in protein molecular surfaces 54 Yamuna Kalyani Mathiharan Domain swapping and protein symmetry—Investigations on the stationary phase survival protein SurE as a model 55 William McLaughlin A searchable set of predictions of protein functions with associated probabilities as derived from annotations of protein sequences and three-dimensional structures 56 Wenli Meng Unfolded proteins can form long range contacts under strongly denaturing conditions in the absence of significant secondary structure 57 Thomas Moon Autoinhibition and salt sensing are linked in the WNK1 kinase 58 Andrew Morin The SBGrid Consortium—Enabling structurally biology computation 59* Chie Motono SAHG, a comprehensive database of predicted structures of all human proteins 60* Kensuke Nakamura Structural analysis of BAR domain of Arfaptin in complex with small GTPase Arl1 61 Janet Newman Getting better at crystallisation by learning from the past 62* Ilona Nudelman Observation of intermolecular interactions in large protein complexes by 2D-dou ble difference NOESY—Application to the 44 kDa interferon-receptor complex 63 Åsa Nylander Structural studies of streptococcal adhesins 64 Sang Ho Park Computational docking studies of histone deacetylase 8 (HDAC8) and its inhibitors by AutoDock Vina program 65* Aviv Paz Sugar transport inhibition of the sodium galactose transporter 66 Janez Plavec NMR solution-state structures of monomeric and dimeric G-quadruplexes adopted by a sequence from N-myc 67* Pavel Plevka Mechanism of re-organization of flavivirus glycoproteins during maturation 68 Mario Pujato The evolution of robustness involves balancing of local sequence and network architecture level mechanisms 69 Pavlina Rezacova Crystal structures of the effector-binding domain of repressor CggR from Bacillus subtilis reveal ligand-induced structural changes upon binding of several glycolytic intermediates III Poster # Author Poster title 70 Florian Richter A computational method to design backbone conformations featuring predefined interactions 71 Victoria Robinson Elucidating the mechanism of action of the translation factor BipA 72 Aleksandr Sahakyan Protein structures from the perspective of side-chain chemical shifts 73 Stefan Schoebel LidA from Legionella is a Rab-supereffector 74* Masaaki Shiina X–ray crystallographic analysis of Runx1–CBF –Ets1–DNA complex assembled on β the enhancer of T cell receptor chain gene 75 Irena Sieglova Structure of the effector-bindinαg domain of arabinose repressor AraR from Bacillus subtilis 76* Peter Stranges Accurate design of a symmetric homodimer using -strand assembly β 77 Juergen Suehnel The Jena Library of Biological Macromolecules—JenaLib 78 Juergen Suehnel The Jena3D viewer for visualization of biological macromolecules 79* Hiroshi Sugimoto Structure and catalytic mechanism of iron-dependent enzymes 80* Mitsuhiro Takeda Recent progress in a stereo-array isotope labeling (SAIL) method for NMR structure determination 81 Todd Taylor Discriminating thermophilic proteins from their mesophilic analogs 82 Eldon Ulrich The Biological Magnetic Resonance Data Bank (BMRB)
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